Hi,
I'm trying to set up a rat brain template for analysis using the freesurfer tool. Before setting up the complete template I have to process a representable rat dataset with the available human template.
With some much appreciated help I managed to get to the skull strip procedure . But the application ceases its operations at this point with the message:
"White matter intensity 0 is lower than CSF intensity 21. Please examine input images. Will terminate ..."
Evaluation using tkmedit does not show something a proper segmentation of the rat brain, however it does show a proper outline of the brain. Since a rat brain and a human brain are very dissimilar I'm not surprised by the fact that the segmentation is incorrect. However the brain is outlined ok. It is also known that the WM intensity values in the rat dataset is somewhat reduced to the GM structure. Which is not expected by the freesurfer tool, which expects WM to be highest intensity value.
My question is: is there a way of circumventing this problem. For instance by defining the mean intensity values of each tissue class or..
Hope someone can help me?
Thanks!
Mark
Hi Mark,
if wm is darker than gm our tools probably will not work. You might try using the FSL segmentation tools and putting the output of them through our stream for surface-based analysis.
cheers, Bruce
On Mon, 20 Oct 2008, Mark Bouts wrote:
Hi,
I'm trying to set up a rat brain template for analysis using the freesurfer tool. Before setting up the complete template I have to process a representable rat dataset with the available human template.
With some much appreciated help I managed to get to the skull strip procedure . But the application ceases its operations at this point with the message:
"White matter intensity 0 is lower than CSF intensity 21. Please examine input images. Will terminate ..."
Evaluation using tkmedit does not show something a proper segmentation of the rat brain, however it does show a proper outline of the brain. Since a rat brain and a human brain are very dissimilar I'm not surprised by the fact that the segmentation is incorrect. However the brain is outlined ok. It is also known that the WM intensity values in the rat dataset is somewhat reduced to the GM structure. Which is not expected by the freesurfer tool, which expects WM to be highest intensity value.
My question is: is there a way of circumventing this problem. For instance by defining the mean intensity values of each tissue class or..
Hope someone can help me?
Thanks!
Mark
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Mark,
once I had a similar problem on an autopsied brain, where it was very difficult to obtain an MPRAGE-like contrast. So instead, I acquired T2-weighted and inverted it. This gave me contrast very similar to MPRAGE, though my analysis failed anyway, due to too strong bias field. So you might want to give it a try and invert your image intensity.
Best,
Marin
On Monday 20 October 2008 19:48:05 Bruce Fischl wrote:
Hi Mark,
if wm is darker than gm our tools probably will not work. You might try using the FSL segmentation tools and putting the output of them through our stream for surface-based analysis.
cheers, Bruce
Hi,
Ok, I will look into inverting the image as Martin suggested. Is there some background info available on how to put the segmentation input into the surface-based analysis. In case the inversion doesn't work. I'm particularly wondering if I need to have the images in *.mgz file format or would nifti or something of that sort suffice?
Thanks
Mark
Bruce Fischl wrote:
Hi Mark,
if wm is darker than gm our tools probably will not work. You might try using the FSL segmentation tools and putting the output of them through our stream for surface-based analysis.
cheers, Bruce
On Mon, 20 Oct 2008, Mark Bouts wrote:
Hi,
I'm trying to set up a rat brain template for analysis using the freesurfer tool. Before setting up the complete template I have to process a representable rat dataset with the available human template.
With some much appreciated help I managed to get to the skull strip procedure . But the application ceases its operations at this point with the message:
"White matter intensity 0 is lower than CSF intensity 21. Please examine input images. Will terminate ..."
Evaluation using tkmedit does not show something a proper segmentation of the rat brain, however it does show a proper outline of the brain. Since a rat brain and a human brain are very dissimilar I'm not surprised by the fact that the segmentation is incorrect. However the brain is outlined ok. It is also known that the WM intensity values in the rat dataset is somewhat reduced to the GM structure. Which is not expected by the freesurfer tool, which expects WM to be highest intensity value.
My question is: is there a way of circumventing this problem. For instance by defining the mean intensity values of each tissue class or..
Hope someone can help me?
Thanks!
Mark
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Mark Bouts -
Martin Kavec